GenomeInfoDb fails to install
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Entering edit mode
David • 0
@bdd4bc81
Last seen 8 months ago

Installation of the latest "GenomeInfoDb" fails with an error in attempting to extract the zip file. Is this a corrupted file or a problem with my Windows system? All previous installations on this computer proceeded smoothly. All other libraries from the Bioconductor install without a problem. However, without this, the entire Biostrings library is not functional!

# simple installation attempt leads to failure
> BiocManager::install("GenomeInfoDb") 

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'GenomeInfoDb'
trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/GenomeInfoDb_1.28.1.zip'
Content type 'application/zip' length 4160116 bytes (4.0 MB)
downloaded 4.0 MB

The downloaded binary packages are in
     C:\Users\XXXXXX\AppData\Local\Temp\RtmpctdRtV\downloaded_packages
Warning message:
In .inet_warning(msg) : error -3 in extracting from zip file

The two pertinent files, GenomeInfoDbData_1.2.6.targ.gz and GenomeInfoDb_1.28.1.zip1 are in the temp file as indicated above.

sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.1.1      tools_4.1.1
zip GenomeInfoDb • 512 views
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Entering edit mode
@marcel-ramos-7325
Last seen 19 days ago
United States

Hi David,

I am unable to reproduce this error on Windows. Please try again. It may be intermittent.

> BiocManager::install("GenomeInfoDb")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'BiocVersion', 'GenomeInfoDb'
also installing the dependencies ‘bitops’, ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘RCurl’, ‘GenomeInfoDbData’

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/bitops_1.0-7.zip'
Content type 'application/zip' length 42470 bytes (41 KB)
downloaded 41 KB

trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/BiocGenerics_0.38.0.zip'
Content type 'application/zip' length 796381 bytes (777 KB)
downloaded 777 KB

trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/S4Vectors_0.30.0.zip'
Content type 'application/zip' length 2448942 bytes (2.3 MB)
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/IRanges_2.26.0.zip'
Content type 'application/zip' length 2662291 bytes (2.5 MB)
downloaded 2.5 MB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.1/RCurl_1.98-1.4.zip'
Content type 'application/zip' length 3071768 bytes (2.9 MB)
downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/BiocVersion_3.13.1.zip'
Content type 'application/zip' length 9399 bytes
downloaded 9399 bytes

trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/windows/contrib/4.1/GenomeInfoDb_1.28.1.zip'
Content type 'application/zip' length 4160116 bytes (4.0 MB)
downloaded 4.0 MB

package ‘bitops’ successfully unpacked and MD5 sums checked
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘RCurl’ successfully unpacked and MD5 sums checked
package ‘BiocVersion’ successfully unpacked and MD5 sums checked
package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\XXXXXX\AppData\Local\Temp\RtmpmCvICv\downloaded_packages
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/GenomeInfoDbData_1.2.6.tar.gz'
Content type 'application/x-gzip' length 10973004 bytes (10.5 MB)
downloaded 10.5 MB

* installing *source* package 'GenomeInfoDbData' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'GenomeInfoDbData'
    finding HTML links ... done
    GenomeInfoDbData-package                html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)

Here is the session info:

> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.1.1      tools_4.1.1
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Entering edit mode

This seems to be a configuration issue.

Please provide more information regarding your setup. It may be that your username have special characters or spaces and it is interacting with R's unzip.

Best,

Marcel

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